Correlation between mRNAseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16M35P9
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 17990 genes and 17 clinical features across 486 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one genes.

  • 171 genes correlated to 'AGE'.

    • ZNF518B|85460 ,  RANBP17|64901 ,  MSL3L2|151507 ,  HCG11|493812 ,  ASB13|79754 ,  ...

  • 610 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • SLC10A4|201780 ,  CYP26A1|1592 ,  CCL17|6361 ,  EXOC3L2|90332 ,  PLAU|5328 ,  ...

  • 949 genes correlated to 'PATHOLOGY.T.STAGE'.

    • FBXO9|26268 ,  VIPR1|7433 ,  LTF|4057 ,  SPCS3|60559 ,  SLCO2A1|6578 ,  ...

  • 3141 genes correlated to 'PATHOLOGY.N.STAGE'.

    • CBFB|865 ,  CLCNKA|1187 ,  CREB5|9586 ,  PELI1|57162 ,  ZNF346|23567 ,  ...

  • 24 genes correlated to 'PATHOLOGY.M.STAGE'.

    • ST6GALNAC1|55808 ,  THSD1P1|374500 ,  C19ORF76|199800 ,  EDN1|1906 ,  CYP21A2|1589 ,  ...

  • 11 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  NCRNA00183|554203 ,  CA5BP|340591 ,  CYORF15A|246126 ,  CYORF15B|84663 ,  ...

  • 6124 genes correlated to 'HISTOLOGICAL.TYPE'.

    • ITGA3|3675 ,  SFTPB|6439 ,  FN1|2335 ,  ERBB3|2065 ,  UNC5CL|222643 ,  ...

  • 29 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • C6ORF162|57150 ,  BAT2|7916 ,  HCFC1|3054 ,  SMARCA4|6597 ,  IPO4|79711 ,  ...

  • 1675 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • SLC25A42|284439 ,  SLC10A4|201780 ,  SRPX2|27286 ,  BEGAIN|57596 ,  COL1A1|1277 ,  ...

  • 3 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • SHOX2|6474 ,  WNT2|7472 ,  APCDD1L|164284

  • 1926 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

    • PELI1|57162 ,  CBFB|865 ,  CREB5|9586 ,  FAM60A|58516 ,  CLCNKA|1187 ,  ...

  • 2 genes correlated to 'MULTIFOCALITY'.

    • AVPI1|60370 ,  AMDHD2|51005

  • 26 genes correlated to 'TUMOR.SIZE'.

    • C3ORF32|51066 ,  ISLR2|57611 ,  ZC3H10|84872 ,  SLC14A1|6563 ,  FOXI2|399823 ,  ...

  • 38 genes correlated to 'RACE'.

    • XKR9|389668 ,  SEC1|653677 ,  ATAD3C|219293 ,  MKX|283078 ,  LRRC37A2|474170 ,  ...

  • 14 genes correlated to 'ETHNICITY'.

    • SNAPC3|6619 ,  ATG12|9140 ,  ZFP36L1|677 ,  TEC|7006 ,  CHRNA10|57053 ,  ...

  • No genes correlated to 'Time to Death', and 'RADIATIONEXPOSURE'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=171 older N=76 younger N=95
NEOPLASM DISEASESTAGE Kruskal-Wallis test N=610        
PATHOLOGY T STAGE Spearman correlation test N=949 higher stage N=237 lower stage N=712
PATHOLOGY N STAGE Wilcoxon test N=3141 class1 N=3141 class0 N=0
PATHOLOGY M STAGE Kruskal-Wallis test N=24        
GENDER Wilcoxon test N=11 male N=11 female N=0
HISTOLOGICAL TYPE Kruskal-Wallis test N=6124        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=29 yes N=29 no N=0
RADIATIONEXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL EXTENSION Kruskal-Wallis test N=1675        
COMPLETENESS OF RESECTION Kruskal-Wallis test N=3        
NUMBER OF LYMPH NODES Spearman correlation test N=1926 higher number.of.lymph.nodes N=1016 lower number.of.lymph.nodes N=910
MULTIFOCALITY Wilcoxon test N=2 unifocal N=2 multifocal N=0
TUMOR SIZE Spearman correlation test N=26 higher tumor.size N=3 lower tumor.size N=23
RACE Kruskal-Wallis test N=38        
ETHNICITY Wilcoxon test N=14 not hispanic or latino N=14 hispanic or latino N=0
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Months) 0-158.8 (median=15.8)
  censored N = 468
  death N = 14
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

171 genes related to 'AGE'.

Table S2.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 47.21 (16)
  Significant markers N = 171
  pos. correlated 76
  neg. correlated 95
List of top 10 genes differentially expressed by 'AGE'

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
ZNF518B|85460 -0.3423 8.352e-15 1.5e-10
RANBP17|64901 -0.3316 7.375e-14 1.33e-09
MSL3L2|151507 -0.3267 1.496e-13 2.69e-09
HCG11|493812 -0.2902 6.92e-11 1.24e-06
ASB13|79754 0.2832 2.034e-10 3.66e-06
C12ORF52|84934 0.2832 2.04e-10 3.67e-06
IL20RA|53832 0.2779 4.964e-10 8.93e-06
LHFPL4|375323 0.2885 5.385e-10 9.68e-06
ENTPD1|953 -0.2752 6.785e-10 1.22e-05
ST3GAL1|6482 -0.2717 1.127e-09 2.03e-05
Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

610 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 275
  STAGE II 51
  STAGE III 106
  STAGE IV 2
  STAGE IVA 44
  STAGE IVC 6
     
  Significant markers N = 610
List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S5.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
SLC10A4|201780 1.48e-10 2.66e-06
CYP26A1|1592 8.041e-10 1.45e-05
CCL17|6361 1.276e-09 2.29e-05
EXOC3L2|90332 1.691e-09 3.04e-05
PLAU|5328 1.71e-09 3.08e-05
LRRC15|131578 1.925e-09 3.46e-05
WISP2|8839 2.219e-09 3.99e-05
IQCE|23288 2.334e-09 4.2e-05
CCL22|6367 2.726e-09 4.9e-05
UNC5CL|222643 3.599e-09 6.47e-05
Clinical variable #4: 'PATHOLOGY.T.STAGE'

949 genes related to 'PATHOLOGY.T.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.13 (0.88)
  N
  1 139
  2 163
  3 161
  4 21
     
  Significant markers N = 949
  pos. correlated 237
  neg. correlated 712
List of top 10 genes differentially expressed by 'PATHOLOGY.T.STAGE'

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FBXO9|26268 -0.3099 3.138e-12 5.64e-08
VIPR1|7433 -0.3001 1.581e-11 2.84e-07
LTF|4057 -0.2902 7.545e-11 1.36e-06
SPCS3|60559 -0.2884 1.011e-10 1.82e-06
SLCO2A1|6578 -0.2874 1.164e-10 2.09e-06
FAM65C|140876 -0.2817 2.787e-10 5.01e-06
GNG7|2788 -0.2813 2.972e-10 5.35e-06
ITM2A|9452 -0.2798 3.73e-10 6.71e-06
LOC653566|653566 -0.2795 3.916e-10 7.04e-06
SYT15|83849 -0.2792 4.076e-10 7.33e-06
Clinical variable #5: 'PATHOLOGY.N.STAGE'

3141 genes related to 'PATHOLOGY.N.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 221
  class1 218
     
  Significant markers N = 3141
  Higher in class1 3141
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S9.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
CBFB|865 36306 3.874e-20 6.97e-16 0.7536
CLCNKA|1187 12491 2.644e-18 4.76e-14 0.7407
CREB5|9586 35494 9.44e-18 1.7e-13 0.7367
PELI1|57162 35128 9.965e-17 1.79e-12 0.7291
ZNF346|23567 13058 1.048e-16 1.89e-12 0.729
MLEC|9761 13117 1.522e-16 2.74e-12 0.7277
DIRAS2|54769 12865.5 1.933e-16 3.48e-12 0.728
TMEM117|84216 34996 2.289e-16 4.12e-12 0.7264
FN1|2335 34973 2.643e-16 4.75e-12 0.7259
FAM60A|58516 34959 2.885e-16 5.19e-12 0.7256
Clinical variable #6: 'PATHOLOGY.M.STAGE'

24 genes related to 'PATHOLOGY.M.STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 267
  M1 9
  MX 209
     
  Significant markers N = 24
List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
ST6GALNAC1|55808 3.665e-07 0.00659
THSD1P1|374500 1.018e-06 0.0183
C19ORF76|199800 1.41e-06 0.0254
EDN1|1906 1.493e-06 0.0269
CYP21A2|1589 1.61e-06 0.029
C1QTNF7|114905 2.132e-06 0.0384
SELP|6403 2.159e-06 0.0388
MAPRE1|22919 2.463e-06 0.0443
SEMA5B|54437 2.886e-06 0.0519
EIF4H|7458 3.482e-06 0.0626
Clinical variable #7: 'GENDER'

11 genes related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 356
  MALE 130
     
  Significant markers N = 11
  Higher in MALE 11
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 43 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
HDHD1A|8226 3727 1.513e-45 2.72e-41 0.9195
NCRNA00183|554203 4848.5 1.242e-40 2.23e-36 0.8952
CA5BP|340591 9308 5.963e-24 1.07e-19 0.7989
CYORF15A|246126 5418 2.494e-22 4.48e-18 1
CYORF15B|84663 3354 9.843e-16 1.77e-11 1
C2ORF84|653140 30059 3.254e-07 0.00584 0.6513
TFRC|7037 16176 3.753e-07 0.00674 0.6505
C1ORF93|127281 29840 1.016e-06 0.0182 0.6448
LOC90110|90110 29751.5 1.408e-06 0.0253 0.6429
C21ORF7|56911 29579 2.627e-06 0.0471 0.6391
Clinical variable #8: 'HISTOLOGICAL.TYPE'

6124 genes related to 'HISTOLOGICAL.TYPE'.

Table S14.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER SPECIFY 9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 34
     
  Significant markers N = 6124
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
ITGA3|3675 2.316e-34 4.17e-30
SFTPB|6439 6.226e-34 1.12e-29
FN1|2335 3.874e-32 6.97e-28
ERBB3|2065 5.797e-32 1.04e-27
UNC5CL|222643 6.61e-32 1.19e-27
ANXA2P2|304 7.831e-32 1.41e-27
AHNAK2|113146 1.017e-31 1.83e-27
SERPINA1|5265 1.087e-31 1.95e-27
CYP2S1|29785 1.691e-31 3.04e-27
MUC1|4582 2.066e-30 3.71e-26
Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

29 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 14
  YES 472
     
  Significant markers N = 29
  Higher in YES 29
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
C6ORF162|57150 5922 4.315e-07 0.00775 0.8962
BAT2|7916 688 4.403e-07 0.00791 0.8959
HCFC1|3054 705 5.226e-07 0.00939 0.8933
SMARCA4|6597 716 5.836e-07 0.0105 0.8916
IPO4|79711 729 6.645e-07 0.0119 0.8897
AP2A1|160 730 6.712e-07 0.012 0.8895
CUL7|9820 733 6.915e-07 0.0124 0.8891
BAT3|7917 769 9.87e-07 0.0177 0.8836
ENPP3|5169 5701 2.087e-06 0.0375 0.872
POM121C|100101267 849 2.14e-06 0.0384 0.8715
Clinical variable #10: 'RADIATIONEXPOSURE'

No gene related to 'RADIATIONEXPOSURE'.

Table S18.  Basic characteristics of clinical feature: 'RADIATIONEXPOSURE'

RADIATIONEXPOSURE Labels N
  NO 408
  YES 17
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

1675 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S19.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 128
  MODERATE/ADVANCED (T4A) 16
  NONE 323
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 1675
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
SLC25A42|284439 6.557e-14 1.18e-09
SLC10A4|201780 9.035e-14 1.63e-09
SRPX2|27286 1.292e-13 2.32e-09
BEGAIN|57596 2.349e-13 4.22e-09
COL1A1|1277 6.425e-13 1.16e-08
FLRT1|23769 7.446e-13 1.34e-08
ITGA3|3675 1.059e-12 1.9e-08
FN1|2335 1.076e-12 1.94e-08
FOXJ1|2302 1.305e-12 2.35e-08
CCL17|6361 1.426e-12 2.56e-08
Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

3 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S21.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 373
  R1 49
  R2 4
  RX 29
     
  Significant markers N = 3
List of 3 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S22.  Get Full Table List of 3 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
SHOX2|6474 2.624e-06 0.0472
WNT2|7472 6.047e-06 0.109
APCDD1L|164284 1.431e-05 0.257
Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

1926 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S23.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.54 (6.2)
  Significant markers N = 1926
  pos. correlated 1016
  neg. correlated 910
List of top 10 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S24.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
PELI1|57162 0.3945 8.655e-16 1.56e-11
CBFB|865 0.393 1.139e-15 2.05e-11
CREB5|9586 0.3877 2.959e-15 5.32e-11
FAM60A|58516 0.3856 4.27e-15 7.68e-11
CLCNKA|1187 -0.3843 5.336e-15 9.6e-11
TAGLN2|8407 0.3777 1.677e-14 3.02e-10
GPR153|387509 0.3727 3.927e-14 7.06e-10
S100A10|6281 0.3709 5.327e-14 9.58e-10
FECH|2235 -0.3689 7.401e-14 1.33e-09
CSGALNACT2|55454 0.3653 1.353e-13 2.43e-09
Clinical variable #14: 'MULTIFOCALITY'

2 genes related to 'MULTIFOCALITY'.

Table S25.  Basic characteristics of clinical feature: 'MULTIFOCALITY'

MULTIFOCALITY Labels N
  MULTIFOCAL 219
  UNIFOCAL 257
     
  Significant markers N = 2
  Higher in UNIFOCAL 2
  Higher in MULTIFOCAL 0
List of 2 genes differentially expressed by 'MULTIFOCALITY'

Table S26.  Get Full Table List of 2 genes differentially expressed by 'MULTIFOCALITY'

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
AVPI1|60370 34892 6.398e-06 0.115 0.6199
AMDHD2|51005 34767 9.457e-06 0.17 0.6177
Clinical variable #15: 'TUMOR.SIZE'

26 genes related to 'TUMOR.SIZE'.

Table S27.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 2.96 (1.6)
  Significant markers N = 26
  pos. correlated 3
  neg. correlated 23
List of top 10 genes differentially expressed by 'TUMOR.SIZE'

Table S28.  Get Full Table List of top 10 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

SpearmanCorr corrP Q
C3ORF32|51066 -0.2808 2.937e-08 0.000528
ISLR2|57611 -0.265 1.169e-07 0.0021
ZC3H10|84872 -0.2607 1.893e-07 0.00341
SLC14A1|6563 -0.2479 7.603e-07 0.0137
FOXI2|399823 -0.2486 8.621e-07 0.0155
LRRC55|219527 -0.2474 9.165e-07 0.0165
CLDN2|9075 -0.2466 9.972e-07 0.0179
CXCL12|6387 -0.2437 1.18e-06 0.0212
APLNR|187 -0.2381 2.111e-06 0.038
CACNG1|786 0.3467 2.609e-06 0.0469
Clinical variable #16: 'RACE'

38 genes related to 'RACE'.

Table S29.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 48
  BLACK OR AFRICAN AMERICAN 20
  WHITE 319
     
  Significant markers N = 38
List of top 10 genes differentially expressed by 'RACE'

Table S30.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

ANOVA_P Q
XKR9|389668 4.011e-12 7.22e-08
SEC1|653677 3.376e-10 6.07e-06
ATAD3C|219293 6.917e-09 0.000124
MKX|283078 1.757e-08 0.000316
LRRC37A2|474170 2.731e-08 0.000491
UTS2|10911 6.585e-08 0.00118
LOC441294|441294 6.748e-08 0.00121
CTAGE9|643854 9.584e-08 0.00172
WFIKKN1|117166 3.184e-07 0.00573
CTAGE4|100128553 4.097e-07 0.00737
Clinical variable #17: 'ETHNICITY'

14 genes related to 'ETHNICITY'.

Table S31.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 340
     
  Significant markers N = 14
  Higher in NOT HISPANIC OR LATINO 14
  Higher in HISPANIC OR LATINO 0
Methods & Data
Input
  • Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Clinical data file = THCA-TP.merged_data.txt

  • Number of patients = 486

  • Number of genes = 17990

  • Number of clinical features = 17

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)